[FieldTrip] Individual MRI - Atlas

[Yuval Harpaz]

Dear Juan Pablo Neira
I think what has to be done in this case is first to transfer the MRI to
MNI space following steps described here.
http://fieldtrip.fcdonders.nl/development/minimum_norm_estimate_new?s[]=mri&s[]=mni
then you use the transformation in reverse on the atlas so you end up with
an MNI atlas reshaped according to the individual MRI.
then you can set sourceplot to use the atlas and give you names of regions
when using the plot (ortho mode) interactively. you can also generate masks
to color regions etc.
I haven't done it but it should be possible.
Yuval

On 27 April 2012 10:53, Juan Pablo Neira <jpnv2006 at gmail.com> wrote:

> Thank you for your help,
>
> But is there any possibility of not using an MNI (average) brain and
> take advantage of the atlas.?  We are working with individual MRIs and
> we do not want to visualize results in the MNI brain.
>
> We could build an atlas, based on our MRI, with other toolbox.  But
> now we would like to use this atlas in the ft_sourceplot and
> ft_volumelookup functions.
>
> Thanks in advance,
>
> Juan Pablo Neira
>
> On Thu, Apr 26, 2012 at 11:35 PM, Robert Oostenveld
> <r.oostenveld at donders.ru.nl> wrote:
> > Hi Juan
> >
> > You should indeed have the data and the atlas in the same coordinate
> system (e.g. MNI). They don't need to have the same resolution.
> >
> > best
> > Robert
> >
> >
> > On 25 Apr 2012, at 16:39, Juan Pablo Neira wrote:
> >
> >> Hello,
> >>
> >> I would like to know if it is possible to use the ft_sourceplot
> >> function with an individual MRI (coordsys: ctf) and an Atlas
> >>
> >> A tried to use one atlas from the Faq "aal_MNI_V4.img".  After
> >> ft_prepare_atlas the coordinate system was coord:mni.
> >>
> >> When I used the ft_sourceplot function (ortho method), there were some
> >> warnings about labels not found and points outside the atlas, but I
> >> always clicked in inside my MRI.  Should I have my MRI and the atlas
> >> in the same coordinate system (mni)?
> >>
> >> Regards,
> >>
> >> Juan Pablo Neira Vesga
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> >
> >
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-- 

Y.Harpaz

a link to the BIU MEG lab:
http://faculty.biu.ac.il/~goldsa/index.html
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